1. Quantifying Population Extinction and Examining the Effects of Different Mutation Rates Jason Stredwick Farshad Samimi Wei Huang Matt Luciw Matthew Rupp

2. Outline Project Overview and Goals Project Description –Baseline configuration –Experiment design Experiments / Discussion –Copy-point, cosmic-point, insertion and deletion mutation rates –Population size, genome length –Different mutation rates, extinction rates Conclusions

3. Project Overview Mutation rates past a certain point will almost always drive a population to extinction. The questions we posed were the following: –Will extinction always occur at some fixed minimum mutation rate or will it follow some type of probability gradient? –How do different types of mutation rates affect extinction? –What other parameters might affect when a population will go extinct? –For surviving populations, what are the effects of different mutation rates?

4. Project Setup: Baseline Configuration All mutation rates are zero 40 by 40 population size –Initially full of identical organisms Fixed genome length of 100 instructions Death is on –2000 instructions executed (reset when it gives birth) Local replacement birth method Different random number seeds for each run Experiments stopped after 30,000 updates 25 samples per data point, unless otherwise specified

5. Project Setup: Experiment Design To understand the affect of mutation rates on the probability of extinction, a simple mapping of the probability of extinction for each mutation rate type sampled. A mutation type, copy-point, was chosen to test the effects of the genome length and population size parameters on the probability of extinction. Three mutation rates were chosen to determine the effect of genome length and population size. –The effects were studied by varying both parameters independently vs P(e). To tie high mutation rates to commonly used mutation rates, a brief look at the evolution ability was sampled for a few common rates approaching the rates studied in this project. –Evolution ability was studied by looking at the number of tasks completed, and the fitness of the dominant organism.

6. Local replacement birth method problem Local replacement prefers empty cells over occupied cells Death timer is reset after every birth Effectively immortal A single organism was able to survive by only producing children (all broken) and never overwriting itself.

7. Cosmic-point Mutation Cosmic-point mutations means each site in the genome has a chance to mutate every update. Initial population dips of ~900+ tended to survive, while lower dips would proceed to zero. Populations rebounded, though not always completely Sampling some of the trials show that if a population survives, it fitness will also begin to increase and tasks would be evolved

8. Cosmic-point Mutation

9. Insertion and Deletion Mutations

15. Copy-point Mutation Copy-point mutation means that every genome site has a chance of mutating on every divide. Surviving populations would crash to a very small number of organisms (as small as 2) Populations would begin to recover but tended to have an upper bound. Some of the trials were sampled and noted that none did any task. Sampling some of the trials, only one survival method was noted –Due to the local replacement problem, a viable organism would be immortal or would only be replaced by another viable organism.

16. Copy-point mutation rate vs. Probability of Extinction

17. Other factors? Determine the affect of genome length and population size on the probability of extinction. Copy-point mutation rates of 0.3, 0.35, and 0.53 were chosen for contrast based on their P(e) values (high, medium, low)

18. Genome Length vs. Mutation Rate

19. Population Size vs. Mutation Rate

20. Relationship to common mutation rates An examination of copy-point mutations at common values How are dominant fitness and the ability to do tasks affected as mutation rates get larger approaching the high extinction mutation rates? Only 20 trials were taken for each data point, due to time constraints

21. Mutation Rate vs. Number of Tasks

22. Mutation Rate vs. log Fitness

23. Conclusions For copy-point and cosmic-point mutation rates, we observed that there is not a hard boundary but more of a continuum for P(e). While time did not permit further mapping, we expect that curve is more of sigmoid –For copy-point mutation rates higher than 0.6, P(e) goes to 1.0 as the mutation rate goes to 1.0 –For copy-point mutation rates lower then 0.3, P(e) goes to 0.0 as the mutation rate goes to zero Survival may still be high at a copy-point mutation rate of 0.3, but it is still unsuited for evolution purposes Changing from local replacement birth method to mass action birth method would have changed the entire dynamic that was found.

24. Conclusions (Cont.) For insertion and deletion, there was no extinction. –The size of the resulting populations were affected –Use of the deletion only scenario would prove useful for code reduction once an end result has been evolved Genome length and population size did influence P(e) for copy-point mutations. –There is an optimal genome length where P(e) is minimized for a particular mutation rate. –Genome length can only make the probability of survival worse. –On the other hand, larger population sizes increases the survivability of a population

25. Thank You Any Questions?